Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation. Issue 3 (11th February 2019)

• Record Type: Journal Article
• Authors: Chen, Kai; Duan, Wenxiu; Han, Qianqian; Sun, Xuan; Li, Wenqian; Hu, Shuangyun; Wan, Jiajia; Wu, Jiang; Ge, Yushu; Liu, Dan
• Is Part Of: Journal of biomolecular structure & dynamics. Volume 37:Issue 3(2019)
• Page Start: 611
• Page End: 622
• Publication Date: 2019-02-11
• Subjects: MPS1 -- molecular dynamic simulation -- inhibition mechanism -- hot spots; MPS1: protein kinase monopolar spindle 1 -- ATP: adenosine triphosphate -- GTP: guanosine triphosphate -- MM/PBSA: Molecular Mechanics/Poisson–Boltzmann surface area -- MM/GBSA: Molecular Mechanics/Generalized Born Surface Area -- PLK1: Polo-like Kinase 1 -- PDB ID: Protein Data Bank identification -- NPT: constant number, pressure, and temperature -- DSSP: definition of secondary structure of proteins -- RMSD: root mean square deviations -- RMSF: root mean square fluctuations -- HY: hydrophobic interaction; Biomolecules -- Periodicals; Molecular structure -- Periodicals; Molecular Biology -- Periodicals; Biomechanics -- Periodicals; 572
• DOI: 10.1080/07391102.2018.1433552
• Languages: English
• ISSNs: 0739-1102

Abstract

Abstract : Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3, 2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.